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- PDB-8in2: 4,5-DOPA-extradiol-dioxygenase from Beta vulgaris -

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Basic information

Entry
Database: PDB / ID: 8in2
Title4,5-DOPA-extradiol-dioxygenase from Beta vulgaris
Components4,5-DOPA dioxygenase extradiol
KeywordsOXIDOREDUCTASE / DOPA / dioxygenase / betalains
Function / homology
Function and homology information


: / stizolobate synthase / stizolobate synthase activity / pigment biosynthetic process / ferrous iron binding / zinc ion binding / cytoplasm
Similarity search - Function
Extradiol aromatic ring-opening dioxygenase, DODA-type / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase
Similarity search - Domain/homology
: / 4,5-DOPA dioxygenase extradiol
Similarity search - Component
Biological speciesBeta vulgaris (beet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsChiang, C.C. / Hsu, C.H.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)111-2113-M-002-015-MY3 Taiwan
Ministry of Science and Technology (MoST, Taiwan)111-2311-B-002-008-MY3 Taiwan
CitationJournal: J.Agric.Food Chem. / Year: 2025
Title: Structural Insights into 4,5-DOPA Extradiol Dioxygenase from Beta vulgaris : Unraveling the Key Step in Versatile Betalain Biosynthesis.
Authors: Chiang, C.C. / Lu, Y.J. / Liu, J.W. / Lin, S.W. / Chou, C.C. / Lin, C.H. / Chien, I.W. / Hsu, C.H.
History
DepositionMar 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4,5-DOPA dioxygenase extradiol
B: 4,5-DOPA dioxygenase extradiol
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5574
Polymers61,4452
Non-polymers1122
Water1086
1
A: 4,5-DOPA dioxygenase extradiol
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7782
Polymers30,7221
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4,5-DOPA dioxygenase extradiol
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7782
Polymers30,7221
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.873, 95.873, 124.908
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 6 - 268 / Label seq-ID: 6 - 268

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'A'AA
22chain 'B'BB

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Components

#1: Protein 4,5-DOPA dioxygenase extradiol


Mass: 30722.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beta vulgaris (beet) / Gene: DODA / Production host: Escherichia coli (E. coli) / References: UniProt: Q70FG7, stizolobate synthase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium phosphate monobasic, 0.1M Tris pH8.5, 50% (w/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.08→30 Å / Num. obs: 12735 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 66.62 Å2 / CC1/2: 0.9792 / Net I/σ(I): 40.4
Reflection shellResolution: 3.08→3.21 Å / Num. unique obs: 1254 / CC1/2: 0.92 / CC star: 0.979

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.08→27.02 Å / SU ML: 0.3279 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.1703
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.22 1265 9.96 %
Rwork0.1671 11430 -
obs0.1725 12695 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.69 Å2
Refinement stepCycle: LAST / Resolution: 3.08→27.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4114 0 2 6 4122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01064246
X-RAY DIFFRACTIONf_angle_d1.21795780
X-RAY DIFFRACTIONf_chiral_restr0.0626604
X-RAY DIFFRACTIONf_plane_restr0.0094746
X-RAY DIFFRACTIONf_dihedral_angle_d22.705556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.20.32511350.23841223X-RAY DIFFRACTION97.56
3.2-3.340.30111380.22361241X-RAY DIFFRACTION100
3.35-3.520.26111370.19281258X-RAY DIFFRACTION99.93
3.52-3.740.25431400.17211250X-RAY DIFFRACTION100
3.74-4.030.23851380.1671269X-RAY DIFFRACTION99.86
4.03-4.430.19661410.14661264X-RAY DIFFRACTION99.72
4.43-5.070.1761430.12791283X-RAY DIFFRACTION99.93
5.07-6.370.20011430.17291289X-RAY DIFFRACTION99.86
6.38-27.020.19021500.15871353X-RAY DIFFRACTION99.8

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